I think that the design by Bob Hoekstra represents one of the most (probably the most) interesting SE design developed in the last years.
My question regard it is the following: Is it possible realize a similar circuit utilizing only two stages (...EC99-300B) ?

Hoekstra's direct coupling design can be configured, with a small loss of elegance, for two stages. One need only adjust values to properly bias the tubes, including adding bias circuitry for the ECC99/6L6. To gain a different perspective on this design, you might glance at the following, which is a circuit essentially the same as Hoekstra's except it uses resistor anode loading: